The long-term objective is to examine HIV evolution and immune function in HIV-infected children and adolescents who, following initiation of protease inhibitor containing antiretroviral therapy [ART], reconstitute immunity [Immune success, IS] but fail to control viral replication [viral failure, VF]. Studies will focus on a unique cohort of treated patients who have sustained immune reconstitution in spite of viral loads that would predict disease progression. This outcome group presents a novel paradigm for the investigation of virus/host cell interactions that are likely to lead to novel new therapeutic strategies. The hypothesis underlying the proposal is that ART-induced discordant responses is multifactorial, involving phenotypic properties of the virus, functional integrity of the thymus, and the impact of ongoing viral replication on immunity. To determine the mechanisms involved in VF/IS responses, three specific aims are proposed: Specific Aim 1. To examine the evolutionary dynamics of amino acid substitutions in Gag and protease [PR] within the peripheral blood compartments of VF/IS individuals. Accumulation and modulation of genetic markers in Gag and PR amino acid sequences that develop in VF/IS individual during ART will be used to evaluate: [A.] compartmentalization of viruses in plasma and in CD4 CD45RO T lymphocytes and [B.] reservoirs of virus in CD4 CD45RA T lymphocytes. Specific Aim 2. To identify genetic determinants in gag and PR from VF/IS individuals that contribute preferentially to restricted replication in thymocytes. Recombinant viruses with gag/PR regions derived from discordant patients will be constructed and evaluated in culture to: [A.] compare pre- and post therapy gag/PR regions from viruses from VF/IS individuals with respect to their capacity to replicate in thymocytes and PBMC ex vivo and [B.]map genetic determinants in Gag and PR that contribute to preferential restriction of replicative capacity in thymocytes. Specific Aim 3. To determine the impact of ongoing viral replication on immunity among individuals who have discordant viral and immune outcomes. Specific studies will evaluate: [A.] thymic output, [B.] post thymic T cell activation and differentiation, and [C.] functional immune response to neoantigen between VS/IS and VF/IS outcome groups.